Variant report

Variant	rs58797246
Chromosome Location	chr12:118740652-118740653
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118740466..118742711-chr12:118813102..118814672,2	MCF-7	breast:
2	chr12:118735634..118738198-chr12:118739744..118741334,2	K562	blood:
3	chr12:118728193..118730845-chr12:118739160..118741836,2	K562	blood:

Variant related genes	Relation type
ENSG00000270482	Chromatin interaction
ENSG00000111707	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10507288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948163	1.00[AMR][1000 genomes]
rs16948168	1.00[AMR][1000 genomes]
rs16948171	1.00[AMR][1000 genomes]
rs16948173	1.00[AMR][1000 genomes]
rs16948189	1.00[AMR][1000 genomes]
rs16948195	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948199	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948225	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948245	1.00[AMR][1000 genomes]
rs16948258	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16948259	1.00[AMR][1000 genomes]
rs16948262	1.00[AMR][1000 genomes]
rs17433259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55965100	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56210304	1.00[AMR][1000 genomes]
rs56319724	1.00[AMR][1000 genomes]
rs56743940	1.00[AMR][1000 genomes]
rs56802741	1.00[AMR][1000 genomes]
rs56819745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57170485	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57865918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58340234	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59036425	1.00[AMR][1000 genomes]
rs59558138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60160994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60749048	1.00[AMR][1000 genomes]
rs60917706	1.00[AMR][1000 genomes]
rs7963735	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7963880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7977168	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1038224	chr12:118648415-118791388	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1040061	chr12:118648415-118800437	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1053417	chr12:118688969-118808530	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118676000-118745200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:118693400-118745000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:118702600-118744600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr12:118712400-118745000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:118715000-118741200	Weak transcription	Thymus	Thymus
6	chr12:118719200-118744400	Weak transcription	HSMM	muscle
7	chr12:118720800-118793600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:118722600-118745000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:118726600-118746800	Weak transcription	Lung	lung
10	chr12:118728400-118744400	Weak transcription	NHLF	lung
11	chr12:118731200-118744400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:118732600-118744800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:118732800-118767600	Weak transcription	Primary T cells from cord blood	blood
14	chr12:118733400-118745000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:118735000-118744600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:118735400-118744400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:118735600-118745000	Weak transcription	Primary B cells from cord blood	blood
18	chr12:118736200-118746000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:118736600-118742600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:118737600-118741200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr12:118738000-118742000	Enhancers	NHEK	skin
22	chr12:118738000-118744600	Weak transcription	Fetal Intestine Small	intestine
23	chr12:118738000-118745000	Weak transcription	Small Intestine	intestine
24	chr12:118738200-118741200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:118738200-118744400	Weak transcription	NH-A	brain
26	chr12:118738200-118745200	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:118738200-118761800	Weak transcription	Fetal Lung	lung
28	chr12:118738400-118741200	Weak transcription	Brain Substantia Nigra	brain
29	chr12:118738400-118744800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:118738400-118745000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:118738600-118745200	Weak transcription	Brain Anterior Caudate	brain
32	chr12:118738600-118745600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:118738800-118741600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:118739000-118741800	Enhancers	NHDF-Ad	bronchial
35	chr12:118739000-118744800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:118739200-118741000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:118739200-118749400	Weak transcription	Brain Angular Gyrus	brain
38	chr12:118739400-118743000	Enhancers	GM12878-XiMat	blood
39	chr12:118739600-118740800	Enhancers	A549	lung
40	chr12:118739600-118741000	Enhancers	Hela-S3	cervix
41	chr12:118739600-118741200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:118739600-118741400	Enhancers	HMEC	breast
43	chr12:118739800-118740800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:118739800-118740800	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr12:118739800-118741400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:118740000-118741200	Enhancers	Primary hematopoietic stem cells	blood
47	chr12:118740000-118741200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:118740000-118745000	Weak transcription	K562	blood
49	chr12:118740200-118742400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:118740200-118744600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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